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feat: Thermo Fisher Scientific NanoDrop Eight - add unread data to asm #1096

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feat: Thermo Fisher Scientific NanoDrop Eight - add unread data to asm #1096

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1 change: 1 addition & 0 deletions src/allotropy/allotrope/converter.py
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Original file line number Diff line number Diff line change
Expand Up @@ -112,6 +112,7 @@
"=": "_EQUALS_",
"@": "_AT_",
"'": "_QUOTE_",
"&": "_AMPERSAND_",
# NOTE: this MUST be at the end, or it will break other key replacements.
" ": "_",
}
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2 changes: 2 additions & 0 deletions src/allotropy/parsers/thermo_fisher_nanodrop_eight/nanodrop_eight_structure.py
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Original file line number Diff line number Diff line change
Expand Up @@ -103,6 +103,7 @@ def create(data: SeriesData, header: SeriesData) -> SpectroscopyRow:
and mass_concentration
and unit
else None,
custom_info={**data.get_unread(), **header.get_unread()},
)
)
if spectra_data_cube:
Expand All @@ -113,6 +114,7 @@ def create(data: SeriesData, header: SeriesData) -> SpectroscopyRow:
data_cube=spectra_data_cube,
sample_identifier=sample_id,
location_identifier=location_id,
custom_info={**data.get_unread(), **header.get_unread()},
)
)

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33 changes: 32 additions & 1 deletion tests/parsers/thermo_fisher_nanodrop_eight/testdata/thermo_nanodrop_eight_RNA.json
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Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,17 @@
"absorbance": {
"value": 17.62,
"unit": "mAU"
},
"custom information document": {
"a260/a230": 2.19,
"sample": "ALP096 PBL1",
"username": "GN104564",
"ng/âμl": 704.986,
"weirdextra:": "Blah",
"a260/a280": 2.07,
"andmore": "Blah",
"date": "11/09/2023 14:19",
"serial number": 1234.0
}
},
{
Expand Down Expand Up @@ -75,6 +86,16 @@
"absorbance": {
"value": 17.16,
"unit": "mAU"
},
"custom information document": {
"a260/a230": 1.87,
"sample": "ALP111 PBL1",
"username": "GN104564",
"ng/âμl": 686.535,
"weirdextra:": "Blah",
"a260/a280": 2.07,
"andmore": "Blah",
"date": "11/09/2023 14:19"
}
},
{
Expand Down Expand Up @@ -125,6 +146,16 @@
"absorbance": {
"value": 17.75,
"unit": "mAU"
},
"custom information document": {
"a260/a230": 2.0,
"sample": "651 PBL1",
"username": "GN104564",
"ng/âμl": 710.13,
"weirdextra:": "Blah",
"a260/a280": 2.08,
"andmore": "Blah",
"date": "11/09/2023 14:20"
}
},
{
Expand Down Expand Up @@ -162,7 +193,7 @@
"file name": "thermo_nanodrop_eight_RNA.txt",
"UNC path": "tests/parsers/thermo_fisher_nanodrop_eight/testdata/thermo_nanodrop_eight_RNA.txt",
"ASM converter name": "allotropy_thermo_fisher_scientific_nanodrop_eight",
"ASM converter version": "0.1.62"
"ASM converter version": "0.1.106"
},
"calculated data aggregate document": {
"calculated data document": [
Expand Down
38 changes: 37 additions & 1 deletion tests/parsers/thermo_fisher_nanodrop_eight/testdata/thermo_nanodrop_eight_example01.json
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Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,15 @@
"absorbance": {
"value": -0.008245813102050192,
"unit": "mAU"
},
"custom information document": {
"a260/a230": 0.4716429731601753,
"a260/a280": -43.64513059797263,
"sample name": "Sample 1",
"ng/âμl": -0.4122906551025096,
"date & time": "06/16/2022 04:38:28 PM(-07:00)",
"serial number": "NDE8675309",
"user name": "Jenny"
}
},
{
Expand Down Expand Up @@ -297,6 +306,13 @@
"absorbance": {
"value": -0.01142989429727237,
"unit": "mAU"
},
"custom information document": {
"a260/a230": 0.7474400267787948,
"a260/a280": 3.500264914912444,
"sample name": "Sample 2",
"ng/âμl": -0.5714947148636185,
"date & time": "06/16/2022 04:39:01 PM(-07:00)"
}
},
{
Expand Down Expand Up @@ -565,6 +581,13 @@
"absorbance": {
"value": -0.009565099990167525,
"unit": "mAU"
},
"custom information document": {
"a260/a230": 1.461831081649615,
"a260/a280": -1.0907398987646264,
"sample name": "Abc 3",
"ng/âμl": -0.47825499950837624,
"date & time": "06/16/2022 04:39:39 PM(-07:00)"
}
},
{
Expand Down Expand Up @@ -775,6 +798,13 @@
"absorbance": {
"value": -0.008348743142043702,
"unit": "mAU"
},
"custom information document": {
"a260/a230": 4.223068228732775,
"a260/a280": -0.6241776992561424,
"sample name": "Abc",
"ng/âμl": -0.4174371571021851,
"date & time": "06/16/2022 04:40:39 PM(-07:00)"
}
},
{
Expand Down Expand Up @@ -964,6 +994,12 @@
"absorbance": {
"value": -0.018283710715536472,
"unit": "mAU"
},
"custom information document": {
"a260/a230": 1.340839950170999,
"a260/a280": 2.027763503070494,
"ng/âμl": -0.9141855357768236,
"date & time": "06/16/2022 04:41:11 PM(-07:00)"
}
},
{
Expand Down Expand Up @@ -1289,7 +1325,7 @@
"file name": "thermo_nanodrop_eight_example01.txt",
"UNC path": "tests/parsers/thermo_fisher_nanodrop_eight/testdata/thermo_nanodrop_eight_example01.txt",
"ASM converter name": "allotropy_thermo_fisher_scientific_nanodrop_eight",
"ASM converter version": "0.1.76"
"ASM converter version": "0.1.106"
},
"calculated data aggregate document": {
"calculated data document": [
Expand Down
38 changes: 37 additions & 1 deletion tests/parsers/thermo_fisher_nanodrop_eight/testdata/thermo_nanodrop_eight_example02.json
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Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,15 @@
"absorbance": {
"value": -0.008245813102050192,
"unit": "mAU"
},
"custom information document": {
"a260/a280": -43.64513059797263,
"a260/a230": 0.4716429731601753,
"sample name": "Sample 1",
"date & time": "06/16/2022 04:38:28 PM(-07:00)",
"ng/âμl": -0.4122906551025096,
"serial number": "NDE8675309",
"user name": "Jenny"
}
},
{
Expand Down Expand Up @@ -297,6 +306,13 @@
"absorbance": {
"value": -0.01142989429727237,
"unit": "mAU"
},
"custom information document": {
"a260/a280": 3.500264914912444,
"a260/a230": 0.7474400267787948,
"sample name": "Sample 2",
"date & time": "06/16/2022 04:39:01 PM(-07:00)",
"ng/âμl": -0.5714947148636185
}
},
{
Expand Down Expand Up @@ -565,6 +581,13 @@
"absorbance": {
"value": -0.009565099990167525,
"unit": "mAU"
},
"custom information document": {
"a260/a280": -1.0907398987646264,
"a260/a230": 1.461831081649615,
"sample name": "Abc 3",
"date & time": "06/16/2022 04:39:39 PM(-07:00)",
"ng/âμl": -0.47825499950837624
}
},
{
Expand Down Expand Up @@ -775,6 +798,13 @@
"absorbance": {
"value": -0.008348743142043702,
"unit": "mAU"
},
"custom information document": {
"a260/a280": -0.6241776992561424,
"a260/a230": 4.223068228732775,
"sample name": "Abc",
"date & time": "06/16/2022 04:40:39 PM(-07:00)",
"ng/âμl": -0.4174371571021851
}
},
{
Expand Down Expand Up @@ -964,6 +994,12 @@
"absorbance": {
"value": -0.018283710715536472,
"unit": "mAU"
},
"custom information document": {
"a260/a280": 2.027763503070494,
"a260/a230": 1.340839950170999,
"date & time": "06/16/2022 04:41:11 PM(-07:00)",
"ng/âμl": -0.9141855357768236
}
},
{
Expand Down Expand Up @@ -1289,7 +1325,7 @@
"file name": "thermo_nanodrop_eight_example02.txt",
"UNC path": "tests/parsers/thermo_fisher_nanodrop_eight/testdata/thermo_nanodrop_eight_example02.txt",
"ASM converter name": "allotropy_thermo_fisher_scientific_nanodrop_eight",
"ASM converter version": "0.1.76"
"ASM converter version": "0.1.106"
},
"calculated data aggregate document": {
"calculated data document": [
Expand Down
38 changes: 37 additions & 1 deletion ...rsers/thermo_fisher_nanodrop_eight/testdata/thermo_nanodrop_eight_tab_aligned_header.json
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Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,15 @@
"absorbance": {
"value": -0.008245813102050192,
"unit": "mAU"
},
"custom information document": {
"a260/a280": -43.64513059797263,
"a260/a230": 0.4716429731601753,
"date & time": "06/16/2022 04:38:28 PM(-07:00)",
"sample name": "Sample 1",
"ng/âμl": -0.4122906551025096,
"serial number": "NDE8675309",
"user name": "Jenny"
}
},
{
Expand Down Expand Up @@ -297,6 +306,13 @@
"absorbance": {
"value": -0.01142989429727237,
"unit": "mAU"
},
"custom information document": {
"a260/a280": 3.500264914912444,
"a260/a230": 0.7474400267787948,
"date & time": "06/16/2022 04:39:01 PM(-07:00)",
"sample name": "Sample 2",
"ng/âμl": -0.5714947148636185
}
},
{
Expand Down Expand Up @@ -565,6 +581,13 @@
"absorbance": {
"value": -0.009565099990167525,
"unit": "mAU"
},
"custom information document": {
"a260/a280": -1.0907398987646264,
"a260/a230": 1.461831081649615,
"date & time": "06/16/2022 04:39:39 PM(-07:00)",
"sample name": "Abc 3",
"ng/âμl": -0.47825499950837624
}
},
{
Expand Down Expand Up @@ -775,6 +798,13 @@
"absorbance": {
"value": -0.008348743142043702,
"unit": "mAU"
},
"custom information document": {
"a260/a280": -0.6241776992561424,
"a260/a230": 4.223068228732775,
"date & time": "06/16/2022 04:40:39 PM(-07:00)",
"sample name": "Abc",
"ng/âμl": -0.4174371571021851
}
},
{
Expand Down Expand Up @@ -964,6 +994,12 @@
"absorbance": {
"value": -0.018283710715536472,
"unit": "mAU"
},
"custom information document": {
"a260/a280": 2.027763503070494,
"a260/a230": 1.340839950170999,
"date & time": "06/16/2022 04:41:11 PM(-07:00)",
"ng/âμl": -0.9141855357768236
}
},
{
Expand Down Expand Up @@ -1289,7 +1325,7 @@
"file name": "thermo_nanodrop_eight_tab_aligned_header.txt",
"UNC path": "tests/parsers/thermo_fisher_nanodrop_eight/testdata/thermo_nanodrop_eight_tab_aligned_header.txt",
"ASM converter name": "allotropy_thermo_fisher_scientific_nanodrop_eight",
"ASM converter version": "0.1.76"
"ASM converter version": "0.1.106"
},
"calculated data aggregate document": {
"calculated data document": [
Expand Down
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